#pragma once
class AlignSequence
{

private:
	double secondsToAlign; 

public:
	AlignSequence(void);
	~AlignSequence(void);
	double getTimetoAlign (); 
	int FastAlign (Sequence & Probe, Sequence & Library, int nucleotidesPerHash= 10);
	int InstrumentedAlign (Sequence & Probe, Sequence & Library, int nucleotidesPerHash = 10);
	int Align (Sequence & Probe, Sequence & Library, int nucleotidesPerHash = 10);
	int AlignAMP (Sequence & Probe, Sequence & Library,int nucleotidesPerHash = 10);
	bool CreateLibrary (Sequence & Library); 
};

